https://github.com/pepijn-devries/ECOTOXr
R package that creates a local SQLite build of (and allows querying of) the US EPA ECOTOX database.
https://github.com/pepijn-devries/ECOTOXr
Last synced: about 1 year ago
JSON representation
R package that creates a local SQLite build of (and allows querying of) the US EPA ECOTOX database.
- Host: GitHub
- URL: https://github.com/pepijn-devries/ECOTOXr
- Owner: pepijn-devries
- License: gpl-3.0
- Created: 2021-10-03T13:46:03.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2024-09-20T09:51:17.000Z (over 1 year ago)
- Last Synced: 2024-09-21T05:00:16.177Z (over 1 year ago)
- Language: R
- Homepage: https://pepijn-devries.github.io/ECOTOXr/
- Size: 5.06 MB
- Stars: 9
- Watchers: 2
- Forks: 2
- Open Issues: 3
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- License: LICENSE.md
Awesome Lists containing this project
- open-sustainable-technology - ECOTOXr - Provides access in R to ECOTOX, a comprehensive knowledgebase providing single chemical environmental toxicity data on aquatic and terrestrial species. (Biosphere / Ecological and Environmental Modeling)
README
---
output: github_document
---
```{r, echo = FALSE, message = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-"
)
library(ECOTOXr)
```
# `ECOTOXr`
[](https://github.com/pepijn-devries/ECOTOXr/actions)
[](https://CRAN.R-project.org/package=ECOTOXr)
[](https://cran.r-project.org/web/checks/check_results_ECOTOXr.html)
[](https://pepijn-devries.r-universe.dev/ECOTOXr)
[](https://app.codecov.io/gh/pepijn-devries/ECOTOXr?branch=main)
`ECOTOXr` can be used to explore and analyse data from the [US EPA ECOTOX database](https://cfpub.epa.gov/ecotox/).
More specifically you can:
* Build a local SQLite copy of the [US EPA ECOTOX database](https://cfpub.epa.gov/ecotox/)
* Search and extract data from the local database
* Sanitise raw data from the local database
* Use experimental features to search the online dashboards: [ECOTOX](https://cfpub.epa.gov/ecotox/search.cfm) and
[CompTox](https://comptox.epa.gov/dashboard/batch-search)
## Why use `ECOTOXr`?
The `ECOTOXr` package allows you to search and extract data from the [ECOTOXicological Knowledgebase](https://cfpub.epa.gov/ecotox/)
and import it directly into `R`. This will allow you to formalize and document the search- and extract-procedures in `R` code.
This makes it easier to share and reproduce such procedures and its results. As illustrated
in the graphical abstract below. Moreover, you can directly apply any statistical
analysis offered in `R`.
## Installation
> Get CRAN version
```{r eval=FALSE}
install.packages("ECOTOXr")
```
> Get development version from r-universe
```{r eval=FALSE}
install.packages("ECOTOXr", repos = c("https://pepijn-devries.r-universe.dev", "https://cloud.r-project.org"))
```
## Usage
### Preparing the database
Although `ECOTOXr` has experimental features to search the online database. The package will
reach its full potential when you build a copy of the database on your local machine.
> Download and build a local copy of the latest ASCII export of the US EPA ECOTOX database
```{r eval=FALSE}
download_ecotox_data()
```
### Searching the local database for species and substances
Once built, you can search the local database for species and substances using different strategies.
You can use the build-in search function of this package, or you can write custom queries using
either the simple query language (SQL) or `dplyr` verbs. More details in the following vignettes:
`vignette("searching-ecotox")` and `vignette("ecotox-schema")`.
## Disclaimers
It is the end-users own responsibility to check the quality of collected data, using the original referenced source in order to evaluate its
fitness for use, see also: .
Note that the package maintainer is not affiliated with the US EPA, this package is therefore **not** official US EPA software.
## Code of Conduct
Please note that the ECOTOXr project is released with a [Contributor Code of Conduct](https://pepijn-devries.github.io/ECOTOXr/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
## Resources
* De Vries, P. (2024) ECOTOXr: An R package for reproducible and transparent retrieval of data from EPA's ECOTOX database. _Chemosphere_ 364 143078
* [Manual of the CRAN release](https://CRAN.R-project.org/package=ECOTOXr)
* EPA ECOTOX help
* Olker, Jennifer H.; Elonen, Colleen M.; Pilli, Anne; Anderson, Arne; Kinziger, Brian; Erickson, Stephen; Skopinski, Michael;
Pomplun, Anita; LaLone, Carlie A.; Russom, Christine L.; Hoff, Dale. (2022): The ECOTOXicology Knowledgebase: A Curated Database of
Ecologically Relevant Toxicity Tests to Support Environmental Research and Risk Assessment. _Environmental Toxicology and Chemistry_
41(6) 1520-1539